Mirror repo layout in cloud storage for symlink correctness

[ali5ter]

Summary

• Changes cloud storage directory layout to mirror the repo structure exactly
• Fixes relative links in findings/*.md not resolving in Typora and other apps that resolve symlinks to their real path
• Updates init-symlinks.sh, bootstrap.sh, README.md, and .env.template

What changed

Before — flat layout with library- prefixed names:

$LIBRARY_BASE/
├── library-findings/
├── collection-a/              (PDFs)
├── collection-b/
└── library-indexed/
    ├── collection-a/          (indexed output)
    └── collection-b/

After — mirrors repo layout:

$LIBRARY_BASE/
├── findings/
└── collections/
    ├── collection-a/
    │   ├── pdfs/
    │   └── indexed/
    └── collection-b/
        ├── pdfs/
        └── indexed/

Why

Relative links in findings/*.md use paths like ../collections/NAME/indexed/SLUG/pages/page-N.png.
When apps resolve the findings/ symlink to its real path before computing relative links, ../collections/
resolves to a path that doesn't exist under the old flat layout. The new layout makes the real paths
siblings, so relative links work everywhere.

Breaking change — migration for existing instances

# In cloud storage, rename/move:
mv $LIBRARY_BASE/library-findings        $LIBRARY_BASE/findings
mv $LIBRARY_BASE/NAME                    $LIBRARY_BASE/collections/NAME/pdfs    # per collection
mv $LIBRARY_BASE/library-indexed/NAME    $LIBRARY_BASE/collections/NAME/indexed # per collection

# Remove existing repo symlinks
rm findings
for d in collections/*/; do rm -f "${d}pdfs" "${d}indexed"; done

# Recreate
./init-symlinks.sh

Moves within the same cloud storage account are instant (server-side rename) — no re-upload needed.